Starting phenix.real_space_refine on Thu Jul 2 09:11:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x51_38058/07_2026/8x51_38058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x51_38058/07_2026/8x51_38058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x51_38058/07_2026/8x51_38058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x51_38058/07_2026/8x51_38058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x51_38058/07_2026/8x51_38058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x51_38058/07_2026/8x51_38058.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 40 5.49 5 S 24 5.16 5 C 5064 2.51 5 N 1346 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8095 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3598 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 8, 'TRANS': 431} Chain breaks: 2 Chain: "B" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3640 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 2 Chain: "E" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 423 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "F" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.24, per 1000 atoms: 0.15 Number of scatterers: 8095 At special positions: 0 Unit cell: (117.6, 78.96, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 24 16.00 P 40 15.00 O 1619 8.00 N 1346 7.00 C 5064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 254.1 milliseconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 39.9% alpha, 15.8% beta 20 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.721A pdb=" N VAL A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.971A pdb=" N PHE A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.710A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 394 removed outlier: 3.753A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.914A pdb=" N CYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.728A pdb=" N CYS A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.650A pdb=" N GLU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 502 Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.861A pdb=" N ASP A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 529 removed outlier: 7.394A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 528 " --> pdb=" O MET A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.589A pdb=" N LYS A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 removed outlier: 3.601A pdb=" N GLU A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.551A pdb=" N ARG B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 removed outlier: 3.954A pdb=" N VAL B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.785A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 325 " --> pdb=" O PRO B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 325' Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.989A pdb=" N ALA B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.853A pdb=" N PHE B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.870A pdb=" N LEU B 420 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 421' Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.639A pdb=" N ARG B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 493 removed outlier: 3.697A pdb=" N ARG B 485 " --> pdb=" O ARG B 481 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 487 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 511 through 516 removed outlier: 4.014A pdb=" N ASP B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 528 removed outlier: 7.635A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 527 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 528 " --> pdb=" O MET B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.708A pdb=" N TYR B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 551 removed outlier: 3.851A pdb=" N GLU B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.691A pdb=" N PHE B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS B 563 " --> pdb=" O ASP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 567 through 574 removed outlier: 3.660A pdb=" N GLU B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 572 " --> pdb=" O CYS B 568 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.374A pdb=" N LYS A 150 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU A 286 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 152 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLU A 288 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 154 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 283 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 removed outlier: 8.545A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 6.465A pdb=" N LYS B 150 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU B 286 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 152 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLU B 288 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE B 154 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 283 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.851A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 436 through 437 removed outlier: 3.752A pdb=" N ILE B 465 " --> pdb=" O TYR B 445 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1749 1.33 - 1.45: 1901 1.45 - 1.57: 4545 1.57 - 1.69: 85 1.69 - 1.81: 38 Bond restraints: 8318 Sorted by residual: bond pdb=" C1' DC E 10 " pdb=" N1 DC E 10 " ideal model delta sigma weight residual 1.468 1.553 -0.085 1.40e-02 5.10e+03 3.73e+01 bond pdb=" C3' DT E 20 " pdb=" O3' DT E 20 " ideal model delta sigma weight residual 1.435 1.505 -0.070 1.30e-02 5.92e+03 2.91e+01 bond pdb=" C3' DT F 6 " pdb=" O3' DT F 6 " ideal model delta sigma weight residual 1.435 1.493 -0.058 1.30e-02 5.92e+03 2.02e+01 bond pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.30e-02 5.92e+03 1.71e+01 bond pdb=" C1' DT E 18 " pdb=" N1 DT E 18 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.63e+01 ... (remaining 8313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 10864 2.75 - 5.50: 401 5.50 - 8.24: 67 8.24 - 10.99: 22 10.99 - 13.74: 5 Bond angle restraints: 11359 Sorted by residual: angle pdb=" O4' DC E 10 " pdb=" C4' DC E 10 " pdb=" C3' DC E 10 " ideal model delta sigma weight residual 106.00 101.45 4.55 6.00e-01 2.78e+00 5.75e+01 angle pdb=" C GLU A 471 " pdb=" N ASP A 472 " pdb=" CA ASP A 472 " ideal model delta sigma weight residual 121.54 133.13 -11.59 1.91e+00 2.74e-01 3.68e+01 angle pdb=" O4' DC E 11 " pdb=" C4' DC E 11 " pdb=" C3' DC E 11 " ideal model delta sigma weight residual 106.00 102.36 3.64 6.00e-01 2.78e+00 3.68e+01 angle pdb=" O4' DC E 9 " pdb=" C4' DC E 9 " pdb=" C3' DC E 9 " ideal model delta sigma weight residual 106.00 102.40 3.60 6.00e-01 2.78e+00 3.59e+01 angle pdb=" C ASP A 64 " pdb=" N THR A 65 " pdb=" CA THR A 65 " ideal model delta sigma weight residual 121.54 132.88 -11.34 1.91e+00 2.74e-01 3.52e+01 ... (remaining 11354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 4743 35.32 - 70.65: 212 70.65 - 105.97: 6 105.97 - 141.30: 1 141.30 - 176.62: 4 Dihedral angle restraints: 4966 sinusoidal: 2369 harmonic: 2597 Sorted by residual: dihedral pdb=" CA GLU B 383 " pdb=" C GLU B 383 " pdb=" N LYS B 384 " pdb=" CA LYS B 384 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual -180.00 -153.74 -26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA LEU A 21 " pdb=" C LEU A 21 " pdb=" N ASP A 22 " pdb=" CA ASP A 22 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 4963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1181 0.125 - 0.251: 74 0.251 - 0.376: 10 0.376 - 0.502: 2 0.502 - 0.627: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" P DA F 20 " pdb=" OP1 DA F 20 " pdb=" OP2 DA F 20 " pdb=" O5' DA F 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.83e+00 chirality pdb=" P DA F 19 " pdb=" OP1 DA F 19 " pdb=" OP2 DA F 19 " pdb=" O5' DA F 19 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" CB VAL B 342 " pdb=" CA VAL B 342 " pdb=" CG1 VAL B 342 " pdb=" CG2 VAL B 342 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 1266 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 75 " 0.024 2.00e-02 2.50e+03 4.81e-02 2.32e+01 pdb=" C LEU B 75 " -0.083 2.00e-02 2.50e+03 pdb=" O LEU B 75 " 0.031 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 374 " 0.339 9.50e-02 1.11e+02 1.52e-01 1.42e+01 pdb=" NE ARG B 374 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 374 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 374 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 374 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 468 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ASP A 468 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP A 468 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 469 " 0.015 2.00e-02 2.50e+03 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2300 2.84 - 3.36: 6286 3.36 - 3.87: 13663 3.87 - 4.39: 15708 4.39 - 4.90: 25949 Nonbonded interactions: 63906 Sorted by model distance: nonbonded pdb=" OD1 ASN B 5 " pdb=" OG1 THR B 74 " model vdw 2.328 3.040 nonbonded pdb=" O LYS B 24 " pdb=" OG1 THR B 331 " model vdw 2.356 3.040 nonbonded pdb=" OH TYR B 153 " pdb=" OE1 GLU B 288 " model vdw 2.383 3.040 nonbonded pdb=" OE1 GLU B 291 " pdb=" OG1 THR B 319 " model vdw 2.413 3.040 nonbonded pdb=" NZ LYS A 439 " pdb=" O2 DT F 17 " model vdw 2.432 3.120 ... (remaining 63901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 351 or resid 363 through 575)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 8318 Z= 0.478 Angle : 1.293 13.740 11359 Z= 0.796 Chirality : 0.076 0.627 1269 Planarity : 0.008 0.152 1297 Dihedral : 18.472 176.620 3288 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.33 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.23), residues: 873 helix: -4.10 (0.14), residues: 285 sheet: -0.00 (0.38), residues: 202 loop : -2.33 (0.25), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 51 TYR 0.041 0.003 TYR A 113 PHE 0.036 0.003 PHE A 315 TRP 0.014 0.005 TRP A 126 HIS 0.010 0.002 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.48 ( 8318) covalent geometry : angle 1.29302 / 0.80 (11359) hydrogen bonds : bond 0.17076 / 10.88 ( 278) hydrogen bonds : angle 8.24472 / 5.67 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7807 (ptmm) cc_final: 0.7432 (tttp) REVERT: A 58 SER cc_start: 0.6720 (p) cc_final: 0.6485 (m) REVERT: A 298 MET cc_start: 0.5681 (mtp) cc_final: 0.5359 (tpp) REVERT: A 370 LEU cc_start: 0.8203 (mt) cc_final: 0.7931 (mt) REVERT: B 2 LYS cc_start: 0.7345 (pttp) cc_final: 0.7114 (pttp) REVERT: B 48 LYS cc_start: 0.7032 (mtmm) cc_final: 0.6704 (mtmm) REVERT: B 49 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 68 LYS cc_start: 0.6957 (tppt) cc_final: 0.6529 (mmpt) REVERT: B 285 TYR cc_start: 0.8217 (m-80) cc_final: 0.7304 (m-80) REVERT: B 468 ASP cc_start: 0.7236 (t70) cc_final: 0.7018 (OUTLIER) REVERT: B 479 LYS cc_start: 0.5949 (ttpp) cc_final: 0.5590 (tppt) REVERT: B 545 MET cc_start: 0.6642 (tpp) cc_final: 0.6262 (tpp) outliers start: 0 outliers final: 1 residues processed: 172 average time/residue: 0.4084 time to fit residues: 74.8019 Evaluate side-chains 104 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 415 HIS A 551 ASN B 121 ASN B 295 HIS B 455 ASN B 495 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.206206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183741 restraints weight = 9607.078| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.56 r_work: 0.3857 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8318 Z= 0.168 Angle : 0.732 8.782 11359 Z= 0.406 Chirality : 0.052 0.296 1269 Planarity : 0.004 0.036 1297 Dihedral : 20.819 171.909 1423 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.30 % Favored : 93.24 % Rotamer: Outliers : 2.94 % Allowed : 11.90 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.26), residues: 873 helix: -2.62 (0.22), residues: 301 sheet: 0.26 (0.38), residues: 205 loop : -2.04 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 51 TYR 0.027 0.002 TYR A 113 PHE 0.020 0.002 PHE B 11 TRP 0.008 0.002 TRP B 126 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 8318) covalent geometry : angle 0.73215 / 0.41 (11359) hydrogen bonds : bond 0.05837 / 3.77 ( 278) hydrogen bonds : angle 5.81148 / 3.94 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8044 (ptmm) cc_final: 0.7605 (tttp) REVERT: A 58 SER cc_start: 0.6908 (p) cc_final: 0.6647 (m) REVERT: A 298 MET cc_start: 0.5778 (mtp) cc_final: 0.5541 (tmm) REVERT: A 370 LEU cc_start: 0.8278 (mt) cc_final: 0.8072 (mt) REVERT: A 373 GLU cc_start: 0.7247 (tp30) cc_final: 0.6766 (tp30) REVERT: A 541 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6947 (tttp) REVERT: A 547 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: B 2 LYS cc_start: 0.7269 (pttp) cc_final: 0.7020 (pttt) REVERT: B 48 LYS cc_start: 0.7391 (mtmm) cc_final: 0.7111 (mtmm) REVERT: B 49 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 68 LYS cc_start: 0.7017 (tppt) cc_final: 0.6787 (tppt) REVERT: B 285 TYR cc_start: 0.8156 (m-80) cc_final: 0.7711 (m-80) REVERT: B 305 GLN cc_start: 0.6972 (mt0) cc_final: 0.6402 (tt0) REVERT: B 455 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6801 (t0) REVERT: B 468 ASP cc_start: 0.7225 (t70) cc_final: 0.7010 (OUTLIER) REVERT: B 479 LYS cc_start: 0.6337 (ttpp) cc_final: 0.5989 (tppt) REVERT: B 545 MET cc_start: 0.7002 (tpp) cc_final: 0.6618 (tpp) outliers start: 24 outliers final: 6 residues processed: 121 average time/residue: 0.3869 time to fit residues: 50.1808 Evaluate side-chains 97 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 465 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 69 optimal weight: 1.9990 chunk 83 optimal weight: 0.0470 chunk 70 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 415 HIS A 551 ASN B 337 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.205147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.182430 restraints weight = 9489.675| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.50 r_work: 0.3838 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8318 Z= 0.152 Angle : 0.673 9.292 11359 Z= 0.374 Chirality : 0.051 0.373 1269 Planarity : 0.003 0.026 1297 Dihedral : 20.693 173.204 1423 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.19 % Favored : 93.36 % Rotamer: Outliers : 2.94 % Allowed : 14.36 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.27), residues: 873 helix: -1.60 (0.27), residues: 302 sheet: 0.36 (0.39), residues: 204 loop : -1.92 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 51 TYR 0.026 0.002 TYR A 113 PHE 0.015 0.002 PHE B 11 TRP 0.005 0.001 TRP B 126 HIS 0.008 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 8318) covalent geometry : angle 0.67288 / 0.37 (11359) hydrogen bonds : bond 0.05080 / 3.28 ( 278) hydrogen bonds : angle 5.32930 / 3.60 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.204 Fit side-chains REVERT: A 22 ASP cc_start: 0.7087 (p0) cc_final: 0.6867 (m-30) REVERT: A 48 LYS cc_start: 0.8099 (ptmm) cc_final: 0.7610 (tttp) REVERT: A 58 SER cc_start: 0.7056 (p) cc_final: 0.6766 (m) REVERT: A 87 LYS cc_start: 0.6566 (mmtt) cc_final: 0.6307 (mmtt) REVERT: A 298 MET cc_start: 0.5783 (mtp) cc_final: 0.5530 (tmm) REVERT: A 373 GLU cc_start: 0.7288 (tp30) cc_final: 0.6799 (tp30) REVERT: A 401 ASN cc_start: 0.7660 (m-40) cc_final: 0.7446 (m-40) REVERT: A 541 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6876 (tttp) REVERT: A 547 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: B 2 LYS cc_start: 0.7304 (pttp) cc_final: 0.7089 (pttt) REVERT: B 48 LYS cc_start: 0.7518 (mtmm) cc_final: 0.7318 (mtmm) REVERT: B 49 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7984 (mm-30) REVERT: B 68 LYS cc_start: 0.7066 (tppt) cc_final: 0.6829 (tppt) REVERT: B 116 LYS cc_start: 0.5306 (mmpt) cc_final: 0.5047 (mmmm) REVERT: B 285 TYR cc_start: 0.8142 (m-80) cc_final: 0.7742 (m-80) REVERT: B 305 GLN cc_start: 0.7008 (mt0) cc_final: 0.6470 (tt0) REVERT: B 367 SER cc_start: 0.8237 (p) cc_final: 0.8029 (p) REVERT: B 383 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4905 (pt0) REVERT: B 479 LYS cc_start: 0.6378 (ttpp) cc_final: 0.5953 (tppt) REVERT: B 537 LEU cc_start: 0.7060 (tp) cc_final: 0.6822 (tt) REVERT: B 545 MET cc_start: 0.7150 (tpp) cc_final: 0.6650 (tpp) outliers start: 24 outliers final: 8 residues processed: 114 average time/residue: 0.3642 time to fit residues: 44.5315 Evaluate side-chains 106 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 415 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.203396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.177066 restraints weight = 9643.548| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.84 r_work: 0.3805 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8318 Z= 0.153 Angle : 0.652 7.648 11359 Z= 0.362 Chirality : 0.051 0.406 1269 Planarity : 0.003 0.021 1297 Dihedral : 20.594 171.054 1423 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.19 % Favored : 93.47 % Rotamer: Outliers : 4.05 % Allowed : 14.60 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.28), residues: 873 helix: -0.88 (0.29), residues: 301 sheet: 0.38 (0.39), residues: 204 loop : -1.79 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 51 TYR 0.024 0.002 TYR A 113 PHE 0.015 0.001 PHE A 490 TRP 0.004 0.001 TRP B 126 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8318) covalent geometry : angle 0.65241 / 0.36 (11359) hydrogen bonds : bond 0.04831 / 3.14 ( 278) hydrogen bonds : angle 5.04016 / 3.42 ( 738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.216 Fit side-chains REVERT: A 22 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6888 (p0) REVERT: A 48 LYS cc_start: 0.8078 (ptmm) cc_final: 0.7649 (tttp) REVERT: A 58 SER cc_start: 0.7074 (p) cc_final: 0.6741 (m) REVERT: A 298 MET cc_start: 0.5769 (mtp) cc_final: 0.5477 (tmm) REVERT: A 373 GLU cc_start: 0.7317 (tp30) cc_final: 0.6781 (tp30) REVERT: A 487 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6506 (mtmp) REVERT: A 541 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6864 (tttp) REVERT: A 547 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: A 549 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7213 (m) REVERT: B 2 LYS cc_start: 0.7391 (pttp) cc_final: 0.7126 (pttt) REVERT: B 21 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7010 (pp) REVERT: B 48 LYS cc_start: 0.7580 (mtmm) cc_final: 0.7370 (mtmm) REVERT: B 49 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8099 (mm-30) REVERT: B 68 LYS cc_start: 0.7099 (tppt) cc_final: 0.6828 (tppp) REVERT: B 116 LYS cc_start: 0.5290 (mmpt) cc_final: 0.4210 (tptp) REVERT: B 285 TYR cc_start: 0.8147 (m-80) cc_final: 0.7674 (m-80) REVERT: B 305 GLN cc_start: 0.7014 (mt0) cc_final: 0.6477 (tt0) REVERT: B 479 LYS cc_start: 0.6387 (ttpp) cc_final: 0.5917 (tppt) REVERT: B 524 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6783 (mmt) outliers start: 33 outliers final: 11 residues processed: 116 average time/residue: 0.4180 time to fit residues: 51.7380 Evaluate side-chains 105 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 80 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 415 HIS B 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.203738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.178024 restraints weight = 9639.791| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.71 r_work: 0.3825 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8318 Z= 0.136 Angle : 0.624 6.999 11359 Z= 0.349 Chirality : 0.050 0.372 1269 Planarity : 0.003 0.020 1297 Dihedral : 20.529 170.716 1423 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.73 % Favored : 93.93 % Rotamer: Outliers : 4.54 % Allowed : 15.21 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.28), residues: 873 helix: -0.50 (0.30), residues: 302 sheet: 0.51 (0.39), residues: 202 loop : -1.70 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 296 TYR 0.022 0.001 TYR A 113 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 8318) covalent geometry : angle 0.62377 / 0.35 (11359) hydrogen bonds : bond 0.04512 / 2.97 ( 278) hydrogen bonds : angle 4.84913 / 3.31 ( 738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.237 Fit side-chains REVERT: A 22 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6768 (p0) REVERT: A 48 LYS cc_start: 0.8062 (ptmm) cc_final: 0.7567 (tttp) REVERT: A 58 SER cc_start: 0.7069 (p) cc_final: 0.6732 (m) REVERT: A 289 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: A 298 MET cc_start: 0.5731 (mtp) cc_final: 0.5421 (tmm) REVERT: A 327 GLU cc_start: 0.7739 (pm20) cc_final: 0.7053 (tp30) REVERT: A 373 GLU cc_start: 0.7370 (tp30) cc_final: 0.6828 (tp30) REVERT: A 487 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6498 (mtmp) REVERT: A 532 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: A 541 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6800 (tttp) REVERT: A 547 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: A 549 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7192 (m) REVERT: B 2 LYS cc_start: 0.7390 (pttp) cc_final: 0.7151 (pttt) REVERT: B 21 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7018 (pp) REVERT: B 49 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 68 LYS cc_start: 0.7021 (tppt) cc_final: 0.6774 (tppp) REVERT: B 97 ARG cc_start: 0.5909 (mmm160) cc_final: 0.5501 (mmm160) REVERT: B 116 LYS cc_start: 0.5311 (mmpt) cc_final: 0.4507 (ptmm) REVERT: B 130 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7629 (tm) REVERT: B 141 ASN cc_start: 0.7719 (m-40) cc_final: 0.7502 (m110) REVERT: B 150 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.6967 (ttmm) REVERT: B 285 TYR cc_start: 0.8094 (m-80) cc_final: 0.7625 (m-80) REVERT: B 305 GLN cc_start: 0.6985 (mt0) cc_final: 0.6473 (tt0) REVERT: B 363 ASN cc_start: 0.6926 (m-40) cc_final: 0.6650 (m-40) REVERT: B 479 LYS cc_start: 0.6340 (ttpp) cc_final: 0.5830 (tppt) REVERT: B 503 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6441 (tm-30) REVERT: B 524 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6761 (mmt) outliers start: 37 outliers final: 8 residues processed: 119 average time/residue: 0.4316 time to fit residues: 54.6242 Evaluate side-chains 105 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 415 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.203371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176974 restraints weight = 9513.747| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.79 r_work: 0.3816 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8318 Z= 0.133 Angle : 0.614 7.020 11359 Z= 0.343 Chirality : 0.050 0.370 1269 Planarity : 0.003 0.025 1297 Dihedral : 20.445 170.755 1423 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.73 % Favored : 93.93 % Rotamer: Outliers : 4.29 % Allowed : 16.32 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.29), residues: 873 helix: -0.22 (0.31), residues: 297 sheet: 0.50 (0.39), residues: 204 loop : -1.49 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 51 TYR 0.021 0.001 TYR A 113 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.008 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 8318) covalent geometry : angle 0.61353 / 0.34 (11359) hydrogen bonds : bond 0.04444 / 2.93 ( 278) hydrogen bonds : angle 4.75090 / 3.24 ( 738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.187 Fit side-chains REVERT: A 22 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6817 (p0) REVERT: A 48 LYS cc_start: 0.8058 (ptmm) cc_final: 0.7572 (tttp) REVERT: A 58 SER cc_start: 0.7099 (p) cc_final: 0.6727 (m) REVERT: A 289 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: A 298 MET cc_start: 0.5803 (mtp) cc_final: 0.5425 (tmm) REVERT: A 327 GLU cc_start: 0.7741 (pm20) cc_final: 0.7118 (tp30) REVERT: A 373 GLU cc_start: 0.7404 (tp30) cc_final: 0.6858 (tp30) REVERT: A 532 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7589 (OUTLIER) REVERT: A 541 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6793 (tttp) REVERT: A 549 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.7191 (m) REVERT: B 2 LYS cc_start: 0.7462 (pttp) cc_final: 0.7226 (pttt) REVERT: B 21 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7034 (pp) REVERT: B 48 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7059 (mtmm) REVERT: B 49 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8043 (mm-30) REVERT: B 68 LYS cc_start: 0.7030 (tppt) cc_final: 0.6797 (tppp) REVERT: B 97 ARG cc_start: 0.5924 (mmm160) cc_final: 0.5568 (mmm160) REVERT: B 130 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7608 (tm) REVERT: B 150 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.6984 (ttmm) REVERT: B 305 GLN cc_start: 0.7030 (mt0) cc_final: 0.6474 (tt0) REVERT: B 363 ASN cc_start: 0.6909 (m-40) cc_final: 0.6598 (m-40) REVERT: B 383 GLU cc_start: 0.5001 (OUTLIER) cc_final: 0.4753 (pt0) REVERT: B 479 LYS cc_start: 0.6276 (ttpp) cc_final: 0.5828 (tppt) REVERT: B 503 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: B 524 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6790 (mmt) outliers start: 35 outliers final: 12 residues processed: 110 average time/residue: 0.4276 time to fit residues: 50.1195 Evaluate side-chains 108 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 415 HIS B 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.200969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.174070 restraints weight = 9554.827| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.82 r_work: 0.3784 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8318 Z= 0.161 Angle : 0.649 7.857 11359 Z= 0.359 Chirality : 0.051 0.430 1269 Planarity : 0.003 0.024 1297 Dihedral : 20.390 170.373 1423 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.19 % Favored : 93.47 % Rotamer: Outliers : 4.42 % Allowed : 16.07 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.29), residues: 873 helix: -0.16 (0.30), residues: 302 sheet: 0.50 (0.39), residues: 197 loop : -1.49 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.020 0.002 TYR A 113 PHE 0.016 0.001 PHE A 490 TRP 0.005 0.001 TRP B 126 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 8318) covalent geometry : angle 0.64942 / 0.36 (11359) hydrogen bonds : bond 0.04749 / 3.12 ( 278) hydrogen bonds : angle 4.80516 / 3.28 ( 738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.284 Fit side-chains REVERT: A 22 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6874 (p0) REVERT: A 48 LYS cc_start: 0.8063 (ptmm) cc_final: 0.7565 (tttp) REVERT: A 58 SER cc_start: 0.7066 (p) cc_final: 0.6660 (m) REVERT: A 289 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: A 298 MET cc_start: 0.5851 (mtp) cc_final: 0.5418 (tmm) REVERT: A 327 GLU cc_start: 0.7748 (pm20) cc_final: 0.7180 (tp30) REVERT: A 373 GLU cc_start: 0.7475 (tp30) cc_final: 0.6852 (tp30) REVERT: A 532 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: A 541 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6759 (tttp) REVERT: A 549 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7230 (m) REVERT: B 2 LYS cc_start: 0.7453 (pttp) cc_final: 0.7190 (pttt) REVERT: B 21 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7039 (pp) REVERT: B 48 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7201 (mtmm) REVERT: B 49 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8046 (mm-30) REVERT: B 68 LYS cc_start: 0.7132 (tppt) cc_final: 0.6900 (tppp) REVERT: B 97 ARG cc_start: 0.5951 (mmm160) cc_final: 0.5708 (mmm160) REVERT: B 130 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7666 (tm) REVERT: B 150 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7020 (ttmm) REVERT: B 305 GLN cc_start: 0.7041 (mt0) cc_final: 0.6480 (tt0) REVERT: B 363 ASN cc_start: 0.6852 (m-40) cc_final: 0.6471 (m-40) REVERT: B 383 GLU cc_start: 0.5156 (OUTLIER) cc_final: 0.4926 (pt0) REVERT: B 479 LYS cc_start: 0.6360 (ttpp) cc_final: 0.5865 (tppt) REVERT: B 503 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: B 524 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6835 (mmt) outliers start: 36 outliers final: 11 residues processed: 114 average time/residue: 0.4407 time to fit residues: 53.5190 Evaluate side-chains 112 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 5 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS B 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.203272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176919 restraints weight = 9497.381| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.76 r_work: 0.3821 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8318 Z= 0.128 Angle : 0.610 7.385 11359 Z= 0.340 Chirality : 0.049 0.358 1269 Planarity : 0.002 0.026 1297 Dihedral : 20.363 171.152 1423 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.96 % Favored : 93.70 % Rotamer: Outliers : 3.93 % Allowed : 17.42 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.29), residues: 873 helix: -0.04 (0.30), residues: 305 sheet: 0.29 (0.39), residues: 202 loop : -1.34 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.020 0.001 TYR A 113 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 8318) covalent geometry : angle 0.61034 / 0.34 (11359) hydrogen bonds : bond 0.04325 / 2.87 ( 278) hydrogen bonds : angle 4.69603 / 3.22 ( 738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.199 Fit side-chains REVERT: A 22 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6792 (p0) REVERT: A 48 LYS cc_start: 0.8057 (ptmm) cc_final: 0.7584 (tttp) REVERT: A 58 SER cc_start: 0.7032 (p) cc_final: 0.6624 (m) REVERT: A 289 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: A 298 MET cc_start: 0.5833 (mtp) cc_final: 0.5416 (tmm) REVERT: A 373 GLU cc_start: 0.7448 (tp30) cc_final: 0.6839 (tp30) REVERT: A 549 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7244 (m) REVERT: B 21 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6982 (pp) REVERT: B 48 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7263 (mtmm) REVERT: B 68 LYS cc_start: 0.7036 (tppt) cc_final: 0.6796 (tppp) REVERT: B 97 ARG cc_start: 0.5923 (mmm160) cc_final: 0.5588 (mmm160) REVERT: B 130 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7713 (tm) REVERT: B 141 ASN cc_start: 0.7660 (m-40) cc_final: 0.7450 (m110) REVERT: B 150 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7065 (ttmm) REVERT: B 305 GLN cc_start: 0.7113 (mt0) cc_final: 0.6557 (tt0) REVERT: B 363 ASN cc_start: 0.6897 (m-40) cc_final: 0.6532 (m-40) REVERT: B 383 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4936 (pt0) REVERT: B 479 LYS cc_start: 0.6283 (ttpp) cc_final: 0.5857 (tppt) REVERT: B 503 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: B 524 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6790 (mmt) outliers start: 32 outliers final: 12 residues processed: 103 average time/residue: 0.4173 time to fit residues: 45.9561 Evaluate side-chains 102 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 564 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 71 optimal weight: 0.0980 chunk 90 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.204024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.177727 restraints weight = 9594.315| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.78 r_work: 0.3822 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8318 Z= 0.122 Angle : 0.598 7.670 11359 Z= 0.335 Chirality : 0.049 0.342 1269 Planarity : 0.002 0.024 1297 Dihedral : 20.340 171.094 1423 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.84 % Favored : 93.81 % Rotamer: Outliers : 2.82 % Allowed : 18.90 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.29), residues: 873 helix: 0.08 (0.31), residues: 305 sheet: 0.24 (0.39), residues: 207 loop : -1.28 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.019 0.001 TYR A 113 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 8318) covalent geometry : angle 0.59818 / 0.33 (11359) hydrogen bonds : bond 0.04181 / 2.80 ( 278) hydrogen bonds : angle 4.60364 / 3.16 ( 738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.208 Fit side-chains REVERT: A 22 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6765 (p0) REVERT: A 48 LYS cc_start: 0.8008 (ptmm) cc_final: 0.7537 (tttp) REVERT: A 58 SER cc_start: 0.7014 (p) cc_final: 0.6604 (m) REVERT: A 298 MET cc_start: 0.5835 (mtp) cc_final: 0.5430 (mmm) REVERT: A 373 GLU cc_start: 0.7469 (tp30) cc_final: 0.6848 (tp30) REVERT: A 460 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7005 (mp0) REVERT: A 549 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7204 (m) REVERT: B 21 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7010 (pp) REVERT: B 48 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7386 (mtmm) REVERT: B 68 LYS cc_start: 0.7076 (tppt) cc_final: 0.6859 (tppp) REVERT: B 97 ARG cc_start: 0.5850 (mmm160) cc_final: 0.5635 (mmm160) REVERT: B 130 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7714 (tm) REVERT: B 150 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7064 (ttmm) REVERT: B 305 GLN cc_start: 0.7103 (mt0) cc_final: 0.6496 (tt0) REVERT: B 363 ASN cc_start: 0.6884 (m-40) cc_final: 0.6526 (m-40) REVERT: B 383 GLU cc_start: 0.5134 (OUTLIER) cc_final: 0.4901 (pt0) REVERT: B 479 LYS cc_start: 0.6259 (ttpp) cc_final: 0.5838 (tppt) REVERT: B 503 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: B 524 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6771 (mmt) outliers start: 23 outliers final: 9 residues processed: 96 average time/residue: 0.4300 time to fit residues: 44.1186 Evaluate side-chains 98 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 3.9990 chunk 83 optimal weight: 0.0770 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.0010 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 45 optimal weight: 0.5980 overall best weight: 0.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 415 HIS B 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.205731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179596 restraints weight = 9670.897| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.76 r_work: 0.3848 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8318 Z= 0.116 Angle : 0.589 7.641 11359 Z= 0.328 Chirality : 0.048 0.310 1269 Planarity : 0.002 0.026 1297 Dihedral : 20.348 171.309 1423 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.41 % Favored : 93.24 % Rotamer: Outliers : 2.82 % Allowed : 19.02 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.29), residues: 873 helix: 0.25 (0.31), residues: 304 sheet: 0.22 (0.39), residues: 207 loop : -1.16 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.018 0.001 TYR A 113 PHE 0.012 0.001 PHE A 315 TRP 0.004 0.001 TRP B 126 HIS 0.004 0.000 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 ( 8318) covalent geometry : angle 0.58864 / 0.33 (11359) hydrogen bonds : bond 0.04002 / 2.71 ( 278) hydrogen bonds : angle 4.51220 / 3.10 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.236 Fit side-chains REVERT: A 22 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6717 (p0) REVERT: A 48 LYS cc_start: 0.7997 (ptmm) cc_final: 0.7532 (tttp) REVERT: A 58 SER cc_start: 0.6960 (p) cc_final: 0.6572 (m) REVERT: A 289 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: A 298 MET cc_start: 0.5847 (mtp) cc_final: 0.5450 (mmm) REVERT: A 327 GLU cc_start: 0.7490 (pm20) cc_final: 0.7242 (pp20) REVERT: A 373 GLU cc_start: 0.7447 (tp30) cc_final: 0.6851 (tp30) REVERT: A 549 VAL cc_start: 0.7465 (OUTLIER) cc_final: 0.7228 (m) REVERT: B 21 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7036 (pp) REVERT: B 48 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7282 (ptmt) REVERT: B 68 LYS cc_start: 0.7024 (tppt) cc_final: 0.6791 (tppp) REVERT: B 97 ARG cc_start: 0.5849 (mmm160) cc_final: 0.5561 (mmm160) REVERT: B 130 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7661 (tm) REVERT: B 150 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.6991 (ttmm) REVERT: B 305 GLN cc_start: 0.7081 (mt0) cc_final: 0.6476 (tt0) REVERT: B 363 ASN cc_start: 0.6896 (m-40) cc_final: 0.6538 (m-40) REVERT: B 383 GLU cc_start: 0.4949 (OUTLIER) cc_final: 0.4661 (pm20) REVERT: B 479 LYS cc_start: 0.6242 (ttpp) cc_final: 0.5837 (tppt) REVERT: B 503 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6473 (tm-30) outliers start: 23 outliers final: 8 residues processed: 94 average time/residue: 0.4159 time to fit residues: 41.8206 Evaluate side-chains 92 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 33 optimal weight: 0.0370 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 415 HIS B 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.204017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.177838 restraints weight = 9596.617| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.77 r_work: 0.3824 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8318 Z= 0.127 Angle : 0.601 7.791 11359 Z= 0.334 Chirality : 0.049 0.335 1269 Planarity : 0.003 0.026 1297 Dihedral : 20.345 170.685 1423 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.41 % Favored : 93.24 % Rotamer: Outliers : 3.07 % Allowed : 19.26 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.29), residues: 873 helix: 0.27 (0.31), residues: 308 sheet: 0.25 (0.39), residues: 207 loop : -1.27 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 459 TYR 0.019 0.001 TYR A 113 PHE 0.012 0.001 PHE A 315 TRP 0.005 0.001 TRP B 126 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 ( 8318) covalent geometry : angle 0.60071 / 0.33 (11359) hydrogen bonds : bond 0.04142 / 2.78 ( 278) hydrogen bonds : angle 4.50573 / 3.09 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.77 seconds wall clock time: 34 minutes 58.10 seconds (2098.10 seconds total)